New Dimensions of Research on Actinomycetes: Quest for Next Generation Antibiotics

Starting with the discovery of streptomycin, the promise of natural products research on actinomycetes has been captivat¬ing researchers and offered an array of life-saving antibiotics. However, most of the actinomycetes have received a little attention of researchers beyond isolation and activity screening. Noticeable gaps in genomic information and associated biosynthetic potential of actinomycetes are mainly the reasons for this situation, which has led to a decline in the discovery rate of novel antibiotics. Recent insights gained from genome mining have revealed a massive existence of previously unrecognized biosynthetic potential in actinomycetes. Successive developments in next-generation sequencing, genome editing, analytical separation and high-resolution spectroscopic methods have reinvigorated interest on such actinomycetes and opened new avenues for the discovery of natural and natural-inspired antibiotics. This article describes the new dimensions that have driven the ongoing resurgence of research on actinomycetes with historical background since the commencement in 1940, for the attention of worldwide researchers. Coupled with increasing advancement in molecular and analytical tools and techniques, the discovery of next-generation antibiotics could be possible by revisiting the untapped potential of actinomycetes from different natural sources

Halotolerant rhizobacteria promote growth and enhance salinity tolerance in peanut

Use of Plant growth promoting rhizobacteria (PGPR) is a promising strategy to improve the crop production under optimal or sub-optimal conditions. In the present study, five diazotrophic salt tolerant bacteria were isolated from the roots of a halophyte, Arthrocnemum indicum. The isolates were partially characterized in vitro for plant growth promoting traits and evaluated for their potential to promote growth and enhanced salt tolerance in peanut. The 16S rRNA gene sequence homology indicated that these bacterial isolates belong to the genera, Klebisiella, Pseudomonas, Agrobacterium and Ochrobactrum. All isolates were nifH positive and able to produce indole -3-acetic acid (ranging from 11.5 to 19.1 µg ml-1). The isolates showed phosphate solubilisation activity (ranging from 1.4 to 55.6 µg phosphate /mg dry weight), 1-aminocyclopropane-1-carboxylate deaminase activity (0.1 to 0.31 µmol α-kB/µg protein/h) and were capable of reducing acetylene in acetylene reduction assay (ranging from 0.95 to 1.8 µmol C2H4 mg protein/h). These isolates successfully colonized the peanut roots and were capable of promoting the growth under non-stress condition. A significant increase in total nitrogen (N) content (up to 76%) was observed over the non-inoculated control. All isolates showed tolerance to NaCl ranging from 4-8% in nutrient broth medium. Under salt stress, inoculated peanut seedlings maintained ion homeostasis, accumulated less reactive oxygen species (ROS) and showed enhanced growth compared to non-inoculated seedlings. Overall, the present study has characterized several potential bacterial strains that showed an enhanced growth promotion effect on peanut under control as well as saline conditions. The results show the possibility to reduce chemical fertilizer inputs and may promote the use of bio-inoculants

Insights into richness of PKS and NRPS gene clusters and genome guided bioprospection for bioactive natural products

Advent of next-generation sequencing and genome-mining tools witnessed a rejuvenation of research on Actinobacteria to meet the growing drug-resistance of pathogenic microbes. Therefore, the Actinobacteria present in underexplored environments are being largely studied in recent days. Intertidal areas, which endure regular periods of immersion and emersion, are important in the coastal or estuarine environment and represent an underexplored biological niche that could be of interest for the discovery. In this study, we have evaluated biosynthetic heterogeneity and richness of intertidal Actinobacteria isolated from Diu Island (India) and demonstrated genome mining in selected potential strain to facilitate the discovery of novel bioactive compounds relevant to antibiotics development. A total of 62 strains affiliated with seven different genera, Streptomyces, Micromonospora, Saccharomonospora, Nocardia, Nocardiopsis, Actinomadura, and Glycomyces were studied. The amplified fragment restriction fingerprinting was done by targeting specific domains of polyketide synthase type II (PKS-II) and non-ribosomal peptide synthetase (NRPS) to reveal the biosynthetic potential and functional heterogeneity of Actinobacteria. The restriction profiles were scored as binary data and visualized in UPGMA dendrograms. Notably, strains affiliated with Streptomyces and Nocardiopsis showed relatively high biosynthetic richness and heterogeneity among the actinobacterial strains. Indeed, those that had a close relation in the 16S rRNA gene-based phylogeny also showed significant heterogeneity, which suggested a quite diverse biosynthetic potential even among closely related isolates. Sequence analysis of randomly selected PKS-II and NRPS fragments revealed their relative similarity to naphthoquinone and anthracycline group compound producing strains. Based on the phylogenetic novelty and biosynthetic richness, three streptomycete strains, JJ36, JJ38, and JJ66 were selected, and their genomes were sequenced using Illumina platform. Resulted draft genome sizes were 6.45, 5.89 and 4.83 Mb, respectively. Genome mining of the assembled draft genomes for secondary metabolite biosynthetic gene clusters relevant to bioactive compounds production was performed using antiSMASH. Interestingly, results revealed the presence of a total 183 secondary metabolite biosynthetic gene clusters including 109 putative gene clusters in the three genomes. This genomic data was further mapped with secondary metabolites profile of particular strains and resulted in the identification of novel compounds affiliated with aromatic ketones

Overexpression of a Plasma Membrane-Localized SbSRP-Like Protein Enhances Salinity and Osmotic Stress Tolerance in Transgenic Tobacco

An obligate halophyte, Salicornia brachiata grows in salt marshes and is considered to be a potential resource of salt- and drought-responsive genes. It is important to develop an understanding of the mechanisms behind enhanced salt tolerance. To increase this understanding, a novel SbSRP gene was cloned, characterized, over-expressed, and functionally validated in the model plant Nicotiana tabacum. The genome of the halophyte S. brachiata contains two homologs of an intronless SbSRP gene of 1,262 bp in length that encodes for a stress-related protein. An in vivo localization study confirmed that SbSRP is localized on the plasma membrane. Transgenic tobacco plants (T1) that constitutively over-express the SbSRP gene showed improved salinity and osmotic stress tolerance. In comparison to Wild Type (WT) and Vector Control (VC) plants, transgenic lines showed elevated relative water and chlorophyll content, lower malondialdehyde content, lower electrolyte leakage and higher accumulation of proline, free amino acids, sugars, polyphenols, and starch under abiotic stress treatments. Furthermore, a lower build-up of H2O2 content and superoxide-radicals was found in transgenic lines compared to WT and VC plants under stress conditions. Transcript expression of Nt-APX (ascorbate peroxidase), Nt-CAT (catalase), Nt-SOD (superoxide dismutase), Nt-DREB (dehydration responsive element binding factor), and Nt-AP2 (apetala2) genes was higher in transgenic lines under stress compared to WT and VC plants. The results suggested that overexpression of membrane-localized SbSRP mitigates salt and osmotic stress in the transgenic tobacco plant. It was hypothesized that SbSRP can be a transporter protein to transmit the environmental stimuli downward through the plasma membrane. However, a detailed study is required to ascertain its exact role in the abiotic stress tolerance mechanism. Overall, SbSRP is a potential candidate to be used for engineering salt and osmotic tolerance in crops

Characterization of an exopolysaccharide produced by a marine <i>Enterobacter cloacae</i>

467-471An exopolysaccharide producing marine bacterium, Enterobacter cloacae, was isolated from marine sediment collected from Gujarat coast, India. Chemical investigation of exopolysaccharide (EPS 71 a) revealed that this exopolysaccharide was an acidic polysaccharide containing high amount of uronic acid, fucose and sulfate which is rare for bacterial exopolysaccharides. EPS 71a was found to have fucose, galactose, glucose and glucuronic acid in a molar ratio of 2:1:1:1